Sun 23 Dec 22:22:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:52 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 365 and 0 Target number of residues in the AU: 365 Target solvent content: 0.6386 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4000 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 94.045 3.200 Wilson plot Bfac: 71.18 9471 reflections ( 99.79 % complete ) and 0 restraints for refining 4423 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3152 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3170 (Rfree = 0.000) for 4423 atoms. Found 39 (39 requested) and removed 40 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 4514 seeds are put forward NCS extension: 0 residues added, 4514 seeds are put forward Round 1: 209 peptides, 39 chains. Longest chain 13 peptides. Score 0.346 Round 2: 298 peptides, 43 chains. Longest chain 22 peptides. Score 0.543 Round 3: 306 peptides, 44 chains. Longest chain 19 peptides. Score 0.552 Round 4: 299 peptides, 42 chains. Longest chain 14 peptides. Score 0.556 Round 5: 308 peptides, 37 chains. Longest chain 23 peptides. Score 0.625 Taking the results from Round 5 Chains 39, Residues 271, Estimated correctness of the model 47.6 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7850 restraints for refining 3651 atoms. 6646 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2803 (Rfree = 0.000) for 3651 atoms. Found 21 (32 requested) and removed 23 (16 requested) atoms. Cycle 2: After refmac, R = 0.2746 (Rfree = 0.000) for 3578 atoms. Found 15 (32 requested) and removed 23 (16 requested) atoms. Cycle 3: After refmac, R = 0.2537 (Rfree = 0.000) for 3536 atoms. Found 9 (32 requested) and removed 20 (16 requested) atoms. Cycle 4: After refmac, R = 0.2566 (Rfree = 0.000) for 3509 atoms. Found 12 (31 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2405 (Rfree = 0.000) for 3494 atoms. Found 3 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.25 Search for helices and strands: 0 residues in 0 chains, 3603 seeds are put forward NCS extension: 22 residues added (15 deleted due to clashes), 3625 seeds are put forward Round 1: 295 peptides, 42 chains. Longest chain 29 peptides. Score 0.546 Round 2: 318 peptides, 37 chains. Longest chain 31 peptides. Score 0.645 Round 3: 329 peptides, 41 chains. Longest chain 25 peptides. Score 0.631 Round 4: 326 peptides, 33 chains. Longest chain 29 peptides. Score 0.695 Round 5: 332 peptides, 37 chains. Longest chain 26 peptides. Score 0.672 Taking the results from Round 4 Chains 37, Residues 293, Estimated correctness of the model 64.1 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7302 restraints for refining 3564 atoms. 5947 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2613 (Rfree = 0.000) for 3564 atoms. Found 26 (32 requested) and removed 31 (16 requested) atoms. Cycle 7: After refmac, R = 0.2411 (Rfree = 0.000) for 3544 atoms. Found 13 (31 requested) and removed 22 (15 requested) atoms. Cycle 8: After refmac, R = 0.2346 (Rfree = 0.000) for 3524 atoms. Found 6 (31 requested) and removed 22 (15 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 3498 atoms. Found 11 (31 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2264 (Rfree = 0.000) for 3480 atoms. Found 6 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.24 Search for helices and strands: 0 residues in 0 chains, 3587 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 3608 seeds are put forward Round 1: 296 peptides, 31 chains. Longest chain 25 peptides. Score 0.657 Round 2: 306 peptides, 35 chains. Longest chain 25 peptides. Score 0.640 Round 3: 318 peptides, 34 chains. Longest chain 25 peptides. Score 0.672 Round 4: 322 peptides, 32 chains. Longest chain 28 peptides. Score 0.696 Round 5: 327 peptides, 36 chains. Longest chain 40 peptides. Score 0.671 Taking the results from Round 4 Chains 35, Residues 290, Estimated correctness of the model 64.3 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7476 restraints for refining 3652 atoms. 6160 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2602 (Rfree = 0.000) for 3652 atoms. Found 19 (32 requested) and removed 28 (16 requested) atoms. Cycle 12: After refmac, R = 0.2505 (Rfree = 0.000) for 3624 atoms. Found 10 (32 requested) and removed 16 (16 requested) atoms. Cycle 13: After refmac, R = 0.2592 (Rfree = 0.000) for 3601 atoms. Found 13 (32 requested) and removed 20 (16 requested) atoms. Cycle 14: After refmac, R = 0.2925 (Rfree = 0.000) for 3578 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 15: After refmac, R = 0.2668 (Rfree = 0.000) for 3578 atoms. Found 18 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.23 Search for helices and strands: 0 residues in 0 chains, 3688 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3704 seeds are put forward Round 1: 284 peptides, 36 chains. Longest chain 23 peptides. Score 0.583 Round 2: 312 peptides, 36 chains. Longest chain 24 peptides. Score 0.643 Round 3: 319 peptides, 35 chains. Longest chain 25 peptides. Score 0.665 Round 4: 329 peptides, 32 chains. Longest chain 27 peptides. Score 0.708 Round 5: 313 peptides, 30 chains. Longest chain 45 peptides. Score 0.697 Taking the results from Round 4 Chains 35, Residues 297, Estimated correctness of the model 66.9 % 3 chains (57 residues) have been docked in sequence Building loops using Loopy2018 35 chains (297 residues) following loop building 3 chains (57 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7406 restraints for refining 3652 atoms. 6015 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2818 (Rfree = 0.000) for 3652 atoms. Found 14 (32 requested) and removed 27 (16 requested) atoms. Cycle 17: After refmac, R = 0.2643 (Rfree = 0.000) for 3617 atoms. Found 15 (31 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.3080 (Rfree = 0.000) for 3598 atoms. Found 31 (31 requested) and removed 26 (16 requested) atoms. Cycle 19: After refmac, R = 0.2555 (Rfree = 0.000) for 3594 atoms. Found 6 (30 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2555 (Rfree = 0.000) for 3571 atoms. Found 16 (29 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.25 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3710 seeds are put forward Round 1: 280 peptides, 34 chains. Longest chain 23 peptides. Score 0.594 Round 2: 316 peptides, 37 chains. Longest chain 24 peptides. Score 0.641 Round 3: 311 peptides, 39 chains. Longest chain 26 peptides. Score 0.613 Round 4: 316 peptides, 36 chains. Longest chain 24 peptides. Score 0.651 Round 5: 306 peptides, 34 chains. Longest chain 27 peptides. Score 0.649 Taking the results from Round 4 Chains 40, Residues 280, Estimated correctness of the model 54.1 % 5 chains (78 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7425 restraints for refining 3652 atoms. 6031 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2673 (Rfree = 0.000) for 3652 atoms. Found 19 (29 requested) and removed 22 (16 requested) atoms. Cycle 22: After refmac, R = 0.2592 (Rfree = 0.000) for 3629 atoms. Found 12 (29 requested) and removed 20 (16 requested) atoms. Cycle 23: After refmac, R = 0.2524 (Rfree = 0.000) for 3610 atoms. Found 10 (29 requested) and removed 22 (16 requested) atoms. Cycle 24: After refmac, R = 0.2438 (Rfree = 0.000) for 3590 atoms. Found 6 (29 requested) and removed 19 (16 requested) atoms. Cycle 25: After refmac, R = 0.2406 (Rfree = 0.000) for 3569 atoms. Found 9 (29 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.22 Search for helices and strands: 0 residues in 0 chains, 3676 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3704 seeds are put forward Round 1: 279 peptides, 40 chains. Longest chain 23 peptides. Score 0.529 Round 2: 300 peptides, 37 chains. Longest chain 33 peptides. Score 0.608 Round 3: 308 peptides, 36 chains. Longest chain 21 peptides. Score 0.635 Round 4: 321 peptides, 35 chains. Longest chain 23 peptides. Score 0.669 Round 5: 307 peptides, 35 chains. Longest chain 25 peptides. Score 0.642 Taking the results from Round 4 Chains 36, Residues 286, Estimated correctness of the model 58.3 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7560 restraints for refining 3652 atoms. 6265 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2515 (Rfree = 0.000) for 3652 atoms. Found 18 (29 requested) and removed 20 (16 requested) atoms. Cycle 27: After refmac, R = 0.2499 (Rfree = 0.000) for 3625 atoms. Found 17 (29 requested) and removed 20 (16 requested) atoms. Cycle 28: After refmac, R = 0.2491 (Rfree = 0.000) for 3611 atoms. Found 18 (29 requested) and removed 19 (16 requested) atoms. Cycle 29: After refmac, R = 0.2275 (Rfree = 0.000) for 3596 atoms. Found 9 (29 requested) and removed 16 (16 requested) atoms. Cycle 30: After refmac, R = 0.2382 (Rfree = 0.000) for 3578 atoms. Found 5 (29 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3675 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3701 seeds are put forward Round 1: 264 peptides, 37 chains. Longest chain 24 peptides. Score 0.525 Round 2: 285 peptides, 35 chains. Longest chain 29 peptides. Score 0.595 Round 3: 290 peptides, 36 chains. Longest chain 28 peptides. Score 0.597 Round 4: 281 peptides, 37 chains. Longest chain 29 peptides. Score 0.566 Round 5: 282 peptides, 33 chains. Longest chain 30 peptides. Score 0.609 Taking the results from Round 5 Chains 36, Residues 249, Estimated correctness of the model 43.5 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7745 restraints for refining 3652 atoms. 6625 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2546 (Rfree = 0.000) for 3652 atoms. Found 19 (29 requested) and removed 21 (16 requested) atoms. Cycle 32: After refmac, R = 0.2448 (Rfree = 0.000) for 3632 atoms. Found 16 (29 requested) and removed 17 (16 requested) atoms. Cycle 33: After refmac, R = 0.2229 (Rfree = 0.000) for 3622 atoms. Found 8 (29 requested) and removed 17 (16 requested) atoms. Cycle 34: After refmac, R = 0.2231 (Rfree = 0.000) for 3607 atoms. Found 3 (29 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2182 (Rfree = 0.000) for 3594 atoms. Found 6 (29 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.30 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3710 seeds are put forward Round 1: 247 peptides, 38 chains. Longest chain 27 peptides. Score 0.469 Round 2: 273 peptides, 33 chains. Longest chain 39 peptides. Score 0.589 Round 3: 262 peptides, 35 chains. Longest chain 23 peptides. Score 0.542 Round 4: 263 peptides, 31 chains. Longest chain 21 peptides. Score 0.587 Round 5: 277 peptides, 34 chains. Longest chain 32 peptides. Score 0.588 Taking the results from Round 2 Chains 35, Residues 240, Estimated correctness of the model 38.1 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 8155 restraints for refining 3652 atoms. 7122 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2433 (Rfree = 0.000) for 3652 atoms. Found 14 (29 requested) and removed 17 (16 requested) atoms. Cycle 37: After refmac, R = 0.2513 (Rfree = 0.000) for 3638 atoms. Found 26 (29 requested) and removed 21 (16 requested) atoms. Cycle 38: After refmac, R = 0.2474 (Rfree = 0.000) for 3634 atoms. Found 26 (29 requested) and removed 18 (16 requested) atoms. Cycle 39: After refmac, R = 0.2117 (Rfree = 0.000) for 3625 atoms. Found 7 (29 requested) and removed 17 (16 requested) atoms. Cycle 40: After refmac, R = 0.2044 (Rfree = 0.000) for 3614 atoms. Found 5 (29 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 3701 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3733 seeds are put forward Round 1: 235 peptides, 37 chains. Longest chain 22 peptides. Score 0.448 Round 2: 258 peptides, 34 chains. Longest chain 23 peptides. Score 0.543 Round 3: 261 peptides, 36 chains. Longest chain 24 peptides. Score 0.528 Round 4: 272 peptides, 33 chains. Longest chain 23 peptides. Score 0.587 Round 5: 257 peptides, 35 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 4 Chains 33, Residues 239, Estimated correctness of the model 37.5 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 8050 restraints for refining 3652 atoms. 7031 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2606 (Rfree = 0.000) for 3652 atoms. Found 29 (29 requested) and removed 21 (16 requested) atoms. Cycle 42: After refmac, R = 0.2511 (Rfree = 0.000) for 3651 atoms. Found 29 (29 requested) and removed 19 (16 requested) atoms. Cycle 43: After refmac, R = 0.2428 (Rfree = 0.000) for 3648 atoms. Found 23 (29 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.2105 (Rfree = 0.000) for 3640 atoms. Found 6 (29 requested) and removed 19 (16 requested) atoms. Cycle 45: After refmac, R = 0.2052 (Rfree = 0.000) for 3620 atoms. Found 4 (29 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3748 seeds are put forward Round 1: 221 peptides, 40 chains. Longest chain 15 peptides. Score 0.370 Round 2: 247 peptides, 38 chains. Longest chain 18 peptides. Score 0.469 Round 3: 253 peptides, 37 chains. Longest chain 22 peptides. Score 0.497 Round 4: 254 peptides, 39 chains. Longest chain 27 peptides. Score 0.476 Round 5: 261 peptides, 40 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 216, Estimated correctness of the model 10.4 % 2 chains (24 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2p7i-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (216 residues) following loop building 2 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9471 reflections ( 99.79 % complete ) and 8165 restraints for refining 3652 atoms. 7247 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2502 (Rfree = 0.000) for 3652 atoms. Found 0 (29 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2475 (Rfree = 0.000) for 3627 atoms. Found 0 (29 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2129 (Rfree = 0.000) for 3601 atoms. Found 0 (29 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2070 (Rfree = 0.000) for 3574 atoms. TimeTaking 68.18